I just found everything I need to do everything I WANTED to do with SSH (our wifi doesn't work)
First, download iCommander via Cydia, and on your PC download the latest version of iPhoneBrowser.
Use iPhoneBrowser to browse directories and put files on your iphone/ipod. You can do pretty much everything except change permissions, which, luckily, is the only thing iCommander does well.
The only major problem with iPhoneBrowser is that it does not recognize /Applications because it has an @ sign at the beginning of it (as you can see while using iCommander).
However, the Applications folder is still accessible! Just go to Private/Var/Stash and you will see the Applications folder!
Using this method, you can add or remove applications, roms, themes, etc., and after adding folders or files simply start up iCommander on your iphone/ipod, and change the permissions (if needed).
I don't know if anyone will find this useful, but I was just so happy upon finally piecing it all together that I had to post it.
Okay, another thing worth noting:
If you have the common problem where an app starts then simply crashes, the widely accepted fix is to recursively set the permissions of its .app folder to 775. However, iCommander does not currently support recursively setting permissions, so you have to set the folder to 775, and then inside the folder, set the following (if they're there) to 775:
_CodeSignature/
_CodeSignature/CodeResources
CodeResources
Info.plist
Pkginfo
ResourceRules.plist
(Application Name; no extension)
After that, try the application. if it STILL doesn't work, then set any files that don't have an extension, end in .html, etc. to 775. If it still doesn't work after that... well that's pretty unlikely, but if so then go through and set every file that doesn't have a sound, video, or image extension to 775.
BTW, this mainly applies to app store apps, but finding them is up to you.
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2.0 - Substitute for SSH (Windows)
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